Britain's largest lecturers' union yesterday voted in favour of a boycott of Israeli lecturers and academic institutions who do not publicly dissociate themselves from Israel's "apartheid policies".

Delegates at the annual conference of the National Association of Teachers in Further and Higher Education (Natfhe) in Blackpool narrowly backed the proposal, despite mounting international pressure from those opposed to a boycott, including a petition from more than 5,000 academics and a plea from the Israeli government. The decision was greeted with disappointment and anger by anti-boycott campaigners last night, but Palestinian groups issued declarations of support.

Presented on the final day of the Natfhe conference, the motion criticised "Israeli apartheid policies, including construction of the exclusion wall, and discriminatory educational practices" and invited members to "consider the appropriateness of a boycott of those that do not publicly dissociate themselves from such policies".

After failed efforts to prevent the debate, speakers outlined the litany of difficulties experienced by Palestinian students and lecturers living under occupation, including the number of Palestinian schools shelled by the Israeli army.

"The majority of Israeli academics are either complicit or acquiescent in their government's policies in the occupied territories," said Tom Hickey, a philosophy lecturer from the University of Brighton, member of the union's national executive committee and proposer of the motion. "Turning a blind eye to what an Israeli colleague thinks about the actions of their government is a culpable blindness."

Delegate John Morgan, who seconded the motion, said there was no academic freedom for Palestinians.

But the union's general secretary, Paul Mackney, spoke against the motion: "Most of us are very angry about the occupation of Palestine," he said, "but this isn't the motion and this isn't the way. Any motion to boycott requires the highest level of legitimacy. As far as I can see no more than a couple of branches have discussed this motion. You cannot build a boycott on conference rhetoric."

Natfhe delegate Ronnie Fraser, chair of Academic Friends of Israel, the primary opponents of the motion on the conference floor, said he was "not happy at all", adding that the vote brought "dishonour and sheer ridicule" upon the union.

Last year the Association of University Teachers (AUT) elected to impose an academic boycott on two Israeli universities. But after an international outcry and a revolt by members it reversed the decision.

Yesterday's boycott resolution will have an official shelf life of less than three days, as on Thursday the two unions will merge, forming the world's largest higher education union with more than 110,000 members. The resolution will only be advisory to the new union. But proponents say the Natfhe decision is important and represents a step change in the wider boycott campaign against Israel.

Aharon Ben-Ze'ev of Haifa university told the Guardian he was "very disappointed", adding: "This ... will only serve to impede the peace process and strengthen extremism on both sides. I never say to British colleagues if you don't subscribe to my beliefs I will boycott you."

David Hirsh, an AUT member, added: "It may not have anti-semitic motivations, but if you organise an academic boycott of Israeli Jewish academics but no one else in the world, that is an anti-semitic policy. What's Natfhe going to do? Set up a committee before which Israeli academics will be hauled?"

The Palestinian Campaign for the Academic and Cultural Boycott of Israel sent its support, saying British academics had "proved once again that they are up to the challenge of meeting injustice".

Stephen Rose of the British Committee for the Universities of Palestine, who began the boycott campaign with a letter to the Guardian in 2002, said he was delighted, adding: "We recognise that this has not been an easy decision faced with the extreme pressure put upon the union by outside forces." He said the vote was "a historic step forward" in "helping persuade our Israeli academic colleagues that it is time to cease silent complicity with the illegal acts of the Israeli state".

But he warned that this was likely to be the start rather than the end of the debate. "I expect those people who oppose it to mobilise on UK campuses and around the world in the weeks ahead."

Backstory

The first rumblings of an academic boycott surfaced in 2002 when Stephen Rose, professor of biology at the Open University, wrote to the Guardian arguing for a moratorium on European funding of Israeli research. The campaign gathered pace at last year's AUT conference in Eastbourne where delegates voted to boycott Bar-Ilan and Haifa universities because of their alleged complicity in the Israeli government's policies. The move provoked a storm of international protest and a month later the boycott was overturned at a special conference.